applyFnToGenes |
apply a function to the genotypes (markers) in each gene transcript and/or base pair range |
applyFnToMarkers |
apply a function to the genotypes from a set of markers |
applyFnToRanges |
apply a function to all the genotypes for markers found in several specified ranges |
clean_mega2rtutorial_data |
remove tutorial data |
computeDosage |
computeDosage function |
dbmega2_import |
read Mega2 SQLite database into R |
DOfamSKATRC |
DofamSKATRC call back function |
DOpedgene |
pedgene call back function |
DOSKAT |
SKAT call back function |
dump_mega2rtutorial_data |
dump tutorial data |
getgenotypes |
fetch genotype character matrix for specified markers |
getgenotypesdos |
fetch dosage integer matrix for specified markers |
getgenotypesgenabel |
process the genotype matrix for specified markers and return the corresponding GenABEL genotype matrix |
getgenotypesraw |
fetch genotype integer matrix for specified markers |
init_famSKATRC |
load Mega2 SQLite database and perform initialization for famSKATRC usage |
init_pedgene |
load Mega2 SQLite database and perform initialization for pedgene usage |
init_SKAT |
load Mega2 SQLite database and perform initialization for SKAT usage |
Mega2ENVGenABEL |
generate gwaa.data-class object |
Mega2famSKATRC |
execute the CRAN famSKAT_RC function on a subset of the gene transcripts |
Mega2gdsfmt |
transcode mega2 to gdsfmt/SNP_ARRAY |
Mega2GenABEL |
generate gwaa.data-class object from a *Mega2R* database |
Mega2GenABELtst |
compare two gwaa.data-class objects |
Mega2pedgene |
Execute the pedgene function on a transcript ranges |
Mega2R-TBLS |
Mega2R SQLite3 tables |
Mega2R-TBLSFilter |
Mega2R SQLite3 table filter |
Mega2RVersion |
Mega2R version |
Mega2SKAT |
execute the CRAN SKAT function on a subset of the gene transcripts |
Mega2VCF |
generate a VCF file set for a collection of markers |
mkfam |
assemble pedigree information into a data frame |
mkMarkers |
create "markers" data frame |
mkphenotype |
generate a phenotype data frame |
read.Mega2DB |
load Mega2 database and initialize family data frame and markers data frame |
setAnnotations |
set default name of transcription database and name of database mapping gene name to entrez gene id |
setfam |
replace the pedigree data frame |
setRanges |
set default range data: chromosome and start/end base pair |
showMapNames |
show the association between mapno and mapname |
showMega2ENV |
show Mega2R environment, viz. data frames and related info. |
showPhenoNames |
show the association between index no and phenotype |
TBLS |
Mega2R SQLite3 tables |
TBLSFilter |
Mega2R SQLite3 table filter |
uniqueFamMember |
regenerate fam data frame with unique values in member column |
where_mega2rtutorial_data |
show directory of tutorial data |